Annotation package that provides correspondence between MeSH ID and Entrez Gene ID

Description

This data represents a collection of annotation packages that can be used as a single object named as package name. This object can be used with the standard four accessor method for all AnnotationDbi objects. Namely: columns, keytypes, keys and select. Users are encouraged to read the vignette from the MeSHDbi package for more details.

Usage

MeSH.PCR.db

Author(s)

Itoshi NIKAIDO

Examples

library(MeSH.PCR.db)
MeSH.PCR.db

cls <- columns(MeSH.PCR.db)
cls
kts <- keytypes(MeSH.PCR.db)
kt <- kts[2]
kts
ks <- head(keys(MeSH.PCR.db, keytype=kts[2]))
ks
res <- select(MeSH.PCR.db, keys=ks, columns=cls, keytype=kt)
head(res)

dbconn(MeSH.PCR.db)
dbfile(MeSH.PCR.db)
dbschema(MeSH.PCR.db)
dbInfo(MeSH.PCR.db)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MeSH.PCR.db)
Loading required package: MeSHDbi
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'MeSHDbi'

The following object is masked from 'package:utils':

    packageName

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MeSH.PCR.db/MeSH.PCR.db.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MeSH.PCR.db
> ### Title: Annotation package that provides correspondence between MeSH ID
> ###   and Entrez Gene ID
> ### Aliases: MeSH.PCR.db
> 
> ### ** Examples
> 
> library(MeSH.PCR.db)
> MeSH.PCR.db
[1] "##### class ####"
[1] "MeSHDb"
attr(,"package")
[1] "MeSHDbi"
[1] "##### connection #####"
<SQLiteConnection>
[1] "##### package name #####"
[1] "MeSH.PCR.db"
> 
> cls <- columns(MeSH.PCR.db)
> cls
[1] "CATEGORY" "CHILD"    "PARENT"  
> kts <- keytypes(MeSH.PCR.db)
> kt <- kts[2]
> kts
[1] "CATEGORY" "CHILD"    "PARENT"  
> ks <- head(keys(MeSH.PCR.db, keytype=kts[2]))
> ks
[1] "D004312" "D006119" "D007264" "D008643" "D008646" "D009852"
> res <- select(MeSH.PCR.db, keys=ks, columns=cls, keytype=kt)
> head(res)
  CATEGORY   CHILD  PARENT
1        A D004312 D000005
2        A D006119 D000005
3        A D007264 D000005
4        A D008643 D000005
5        A D008646 D000005
6        A D009852 D000005
> 
> dbconn(MeSH.PCR.db)
<SQLiteConnection>
> dbfile(MeSH.PCR.db)
[1] "/home/ddbj/local/lib64/R/library/MeSH.PCR.db/extdata/MeSH.PCR.db.sqlite"
> dbschema(MeSH.PCR.db)
[1] "CREATE TABLE DATA (\n  PARENT CHAR(7) NOT NULL,\n  CHILD CHAR(7) NOT NULL,\n  CATEGORY CHAR(1) NOT NULL\n)"
[2] "CREATE TABLE METADATA (\n  NAME VARCHAR(80),\n  VALUE VARCHAR(255)\n)"                                     
> dbInfo(MeSH.PCR.db)
             NAME                                     VALUE
1      SOURCEDATE                               10-Feb-2016
2      SOURCENAME                  Medical Subject Headings
3       SOURCEURL http://www.nlm.nih.gov/mesh/filelist.html
4        DBSCHEMA                               MeSH.PCR.db
5 DBSCHEMAVERSION                                       1.0
6     MESHVERSION                                      2016
7         package                               MeSH.PCR.db
8         Db type                               MeSH.PCR.db
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>